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- PDB-3v4h: Crystal structure of a type VI secretion system effector from Yer... -

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Basic information

Entry
Database: PDB / ID: 3v4h
TitleCrystal structure of a type VI secretion system effector from Yersinia pestis
Componentshypothetical protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyHcp1-like / : / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / Mainly Beta / Hcp1 family type VI secretion system effector
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFilippova, E.V. / Halavaty, A. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of a type VI secretion system effector from Yersinia pestis
Authors: Filippova, E.V. / Halavaty, A. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)41,3942
Polymers41,3942
Non-polymers00
Water46826
1
A: hypothetical protein
B: hypothetical protein

A: hypothetical protein
B: hypothetical protein

A: hypothetical protein
B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)124,1836
Polymers124,1836
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12050 Å2
ΔGint-96 kcal/mol
Surface area36320 Å2
MethodPISA
2
A: hypothetical protein
B: hypothetical protein
x 6


Theoretical massNumber of molelcules
Total (without water)248,36612
Polymers248,36612
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area30280 Å2
ΔGint-212 kcal/mol
Surface area66450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.550, 148.550, 82.573
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.504605, -0.863349, -0.001507), (0.863345, 0.504607, -0.002585), (0.002992, 3.0E-6, 0.999996)-0.03803, 0.0568, 0.01183

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Components

#1: Protein hypothetical protein


Mass: 20697.156 Da / Num. of mol.: 2 / Fragment: UNP residues 29-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: y1547, YPO2937, YP_2759 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 "magic" / References: UniProt: Q8CLE0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M Citric acid, 1.4 M Ammonium Sulfate, 25% sucrose, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2011 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 20196 / Num. obs: 20196 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 65.7 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.473
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.4 / Num. unique all: 890 / % possible all: 87.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y12

1y12


Resolution: 2.1→29.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.904 / SU ML: 0.169 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26857 1042 5.2 %RANDOM
Rwork0.21619 ---
obs0.21887 19150 98.61 %-
all-19150 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.202 Å2
Baniso -1Baniso -2Baniso -3
1--3.29 Å2-1.64 Å20 Å2
2---3.29 Å20 Å2
3---4.93 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 0 26 2114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022148
X-RAY DIFFRACTIONr_bond_other_d0.0020.021451
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9392889
X-RAY DIFFRACTIONr_angle_other_deg0.87733540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.055254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.58124.66103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.73515390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2421510
X-RAY DIFFRACTIONr_chiral_restr0.1010.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022324
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02438
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 62 -
Rwork0.286 1227 -
obs--88.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.00720.1429-0.35592.6540.03121.91740.1189-0.4023-0.29740.1725-0.0433-0.8033-0.02640.181-0.07560.2836-0.0516-0.21150.30570.01770.361229.86880.889916.3185
22.9531.2009-0.28455.5272-0.51730.96550.0793-0.36-0.06530.28460.0358-0.26160.03960.0041-0.11510.1701-0.0466-0.15990.2403-0.01560.176327.48325.460817.5084
32.61790.6493-0.77313.5707-0.0922.0808-0.1074-0.3171-0.91550.445-0.1381-0.6920.12480.28710.24550.30730.0207-0.11820.24620.25250.52515.7479-25.737715.9096
46.32941.6465-1.79681.64050.64771.79380.0312-0.2888-0.52310.3141-0.0425-0.48770.02970.24360.01130.3881-0.02-0.15360.19830.2130.460818.3296-21.136217.7718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 95
2X-RAY DIFFRACTION2A96 - 155
3X-RAY DIFFRACTION3B4 - 95
4X-RAY DIFFRACTION4B96 - 155

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